Check simulation sim_4.5
Alessio Crippa
12 February, 2019
Dynamic report for checking simulation design (4.5)
True mean Progression Free Time (PFT)
Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
---- 7.11 7.11 7.11 7.11 7.11
---+ 7.11 7.11 7.11 7.11 7.11
--+- 7.11 7.11 7.11 7.11 7.11
--++ 7.11 7.11 7.11 7.11 7.11
-+-- 7.11 7.11 7.11 7.11 7.11
-+-+ 7.11 7.11 7.11 7.11 7.11
-++- 7.11 7.11 7.11 7.11 7.11
-+++ 7.11 7.11 7.11 7.11 7.11
+--- 7.11 7.11 7.11 7.11 7.11
+--+ 7.11 7.11 7.11 7.11 7.11
+-+- 7.11 7.11 7.11 7.11 7.11
+-++ 7.11 7.11 7.11 7.11 7.11
++-- 7.11 7.11 7.11 7.11 7.11
++-+ 7.11 7.11 7.11 7.11 7.11
+++- 7.11 7.11 7.11 7.11 7.11Graduation output
$superiority
Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all 0 0 0 0 0
TP53- & AR- 0 0 0 0 0
TP53+ 0 0 0 0 0
DRD+ 0 0 0 0 0
TEfus+ 0 0 0 0 0
$inferiority
Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all 0 0 0 0 0
TP53- & AR- 0 0 0 0 0
TP53+ 0 0 0 0 0
DRD+ 0 0 0 0 0
TEfus+ 0 0 0 0 0Final probability of superioriry by signatures and biomarkers subtypes
$p_sign
Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all 0.46 0.28 0.39 0.34 0.32
TP53- & AR- 0.68 0.35 0.20 0.55 0.60
TP53+ 0.42 0.41 0.41 0.41 0.37
DRD+ 0.12 0.14 0.17 0.14 0.20
TEfus+ 0.36 0.25 0.39 0.28 0.21
$p_type
Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
---- 1.00 0.89 0.49 0.98 0.94
---+ 0.80 0.61 0.70 0.82 0.34
--+- 0.50 0.77 0.67 0.39 0.49
--++ 0.87 0.52 0.52 0.72 0.64
-+-- 0.16 0.14 0.09 0.23 0.46
-+-+ 0.43 0.42 0.34 0.29 0.55
-++- 0.54 0.48 0.63 0.61 0.48
-+++ 0.11 0.15 0.13 0.19 0.13
+--- 0.91 0.53 0.67 0.80 0.74
+--+ 0.26 0.32 0.64 0.23 0.22
+-+- 0.51 0.49 0.51 0.52 0.58
+-++ 0.55 0.57 0.61 0.58 0.60
++-- 0.16 0.29 0.45 0.21 0.16
++-+ 0.41 0.48 0.54 0.36 0.45
+++- 0.54 0.55 0.48 0.44 0.52
Control Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
---- 98 86 71 31 74 61
---+ 15 6 7 12 16 10
--+- 39 37 27 30 24 27
--++ 14 22 18 8 21 20
-+-- 18 5 5 10 6 16
-+-+ 8 8 12 8 6 13
-++- 0 3 1 4 1 1
-+++ 3 1 0 3 2 1
+--- 10 11 6 5 9 8
+--+ 4 5 6 8 8 7
+-+- 0 1 0 0 1 3
+-++ 8 6 3 3 5 4
++-- 11 3 3 4 2 3
++-+ 2 2 4 3 1 0
+++- 4 0 3 4 1 0 Control Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all 234 196 166 133 177 174
TP53- & AR- 139 105 95 61 102 100
TP53+ 68 70 52 52 55 56
DRD+ 46 22 28 36 19 34
TEfus+ 54 50 50 45 59 55
Number of events, PT, and rate by subtype (over time)
Number of events, PT, and rate by signature (over time)
Analysis of final simulated results
Sample of 10 rows:
id trt trt2 line subtype delta month0 time_m all TP53- & AR- TP53+ DRD+ TEfus+
790 720 Docetaxel Docetaxel 1 +-++ 1 23 7.5639230 1 0 1 0 1
272 252 Abiraterone Abiraterone 1 ---- 1 8 4.5849921 1 1 0 0 0
13 13 Enzalutamide Enzalutamide 1 --++ 1 0 16.2484093 1 0 1 0 1
804 731 Enzalutamide Enzalutamide 1 --++ 0 24 12.0000000 1 0 1 0 1
719 654 Cabazitaxel Cabazitaxel 1 ---- 1 21 4.6382168 1 1 0 0 0
930 845 Control Enzalutamide 1 ++-- 1 28 2.9078370 1 0 0 1 0
931 846 Control Docetaxel 1 ++-- 1 28 0.9312359 1 0 0 1 0
186 172 Cabazitaxel Cabazitaxel 1 --+- 1 5 10.1360198 1 0 1 0 0
55 55 Cabazitaxel Cabazitaxel 1 --+- 1 1 8.4867349 1 0 1 0 0
1010 919 Cabazitaxel Cabazitaxel 1 ---- 0 30 6.0000000 1 1 0 0 0Descriptives
Mean number of progressions and follow-up time:
$all
# A tibble: 6 x 4
trt progressions PT rate
<fct> <dbl> <dbl> <dbl>
1 Control 216 1524. 0.142
2 Enzalutamide 180 1555. 0.116
3 Abiraterone 142 1032. 0.138
4 Carboplatin 117 842. 0.139
5 Cabazitaxel 163 1242. 0.131
6 Docetaxel 151 1120. 0.135
$`TP53- & AR-`
# A tibble: 6 x 4
trt progressions PT rate
<fct> <dbl> <dbl> <dbl>
1 Control 129 874. 0.148
2 Enzalutamide 91 863. 0.105
3 Abiraterone 83 609. 0.136
4 Carboplatin 58 351. 0.165
5 Cabazitaxel 92 759. 0.121
6 Docetaxel 82 668. 0.123
$`TP53+`
# A tibble: 6 x 4
trt progressions PT rate
<fct> <dbl> <dbl> <dbl>
1 Control 62 471. 0.132
2 Enzalutamide 67 543. 0.123
3 Abiraterone 41 328. 0.125
4 Carboplatin 41 329. 0.125
5 Cabazitaxel 50 374. 0.134
6 Docetaxel 52 378. 0.137
$`DRD+`
# A tibble: 6 x 4
trt progressions PT rate
<fct> <dbl> <dbl> <dbl>
1 Control 34 381. 0.0892
2 Enzalutamide 23 147. 0.157
3 Abiraterone 27 193. 0.140
4 Carboplatin 32 235. 0.136
5 Cabazitaxel 17 109. 0.156
6 Docetaxel 28 245. 0.114
$`TEfus+`
# A tibble: 6 x 4
trt progressions PT rate
<fct> <dbl> <dbl> <dbl>
1 Control 49 361. 0.136
2 Enzalutamide 50 399. 0.125
3 Abiraterone 47 310. 0.152
4 Carboplatin 39 294. 0.133
5 Cabazitaxel 54 381. 0.142
6 Docetaxel 54 342. 0.158
Kaplan-Meier results:
$all
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)
n events median 0.95LCL 0.95UCL
trt=Control 259 216 5.10 4.11 6.29
trt=Enzalutamide 216 180 6.05 5.01 7.34
trt=Abiraterone 178 142 5.21 4.41 6.63
trt=Carboplatin 147 117 5.81 4.29 7.23
trt=Cabazitaxel 198 163 5.23 4.44 6.24
trt=Docetaxel 190 151 5.74 4.92 6.97
$`TP53- & AR-`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)
n events median 0.95LCL 0.95UCL
trt=Control 152 129 5.06 3.57 6.39
trt=Enzalutamide 115 91 6.62 5.89 8.38
trt=Abiraterone 101 83 5.39 4.49 7.66
trt=Carboplatin 69 58 3.46 2.34 6.78
trt=Cabazitaxel 115 92 5.60 4.41 7.78
trt=Docetaxel 108 82 6.44 4.92 8.48
$`TP53+`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)
n events median 0.95LCL 0.95UCL
trt=Control 75 62 5.71 3.63 7.09
trt=Enzalutamide 76 67 4.83 4.06 7.60
trt=Abiraterone 56 41 5.83 3.77 8.26
trt=Carboplatin 56 41 6.86 4.57 9.08
trt=Cabazitaxel 60 50 5.23 4.44 9.16
trt=Docetaxel 63 52 5.74 4.45 7.69
$`DRD+`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)
n events median 0.95LCL 0.95UCL
trt=Control 50 34 7.86 6.29 11.24
trt=Enzalutamide 25 23 5.94 4.28 8.35
trt=Abiraterone 31 27 4.41 2.88 9.19
trt=Carboplatin 43 32 5.79 3.39 8.68
trt=Cabazitaxel 20 17 2.28 1.56 NA
trt=Docetaxel 36 28 5.24 2.96 12.78
$`TEfus+`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)
n events median 0.95LCL 0.95UCL
trt=Control 59 49 5.73 3.46 7.65
trt=Enzalutamide 59 50 5.59 4.04 8.39
trt=Abiraterone 56 47 5.39 3.55 7.15
trt=Carboplatin 50 39 5.93 2.37 9.08
trt=Cabazitaxel 65 54 4.44 3.76 7.37
trt=Docetaxel 62 54 4.86 2.68 6.95
